yml file updated

astrocyte_package.yml

@@ -17,7 +17,7 @@ title: 'BICF ChIP-seq Analysis Workflow'
 # A summary of the workflow package in plain text
 description: |
   This is a workflow package for the BioHPC/BICF ChIP-seq workflow system.
-  It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker MAnorm and HOMER, visualization application.
+  It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, visualization application.
 
 # -----------------------------------------------------------------------------
 # DOCUMENTATION
@@ -76,22 +76,13 @@ workflow_modules:
 
 workflow_parameters:
 
-  - id: bams
-    type: files
-    required: true
-    description: |
-      One or more BAM alignments from a ChIP-Seq experiment and a design file with the link between the same name and the sample group. All files will be imported from GreenCenter ChIP-seq peak calling pipeline
-    regex: ".*(bam)*"
-    min: 1
-
-
   - id: design
     type: file
     required: true
     regex: ".*csv"
     description: |
       A design file listing pairs of sample name and sample group.
-      Columns must include: SampleID,SampleName,SampleGroup,FullPathToFqR1,FullPathToFqR2
+      Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller
 
   - id: genome
     type: select
@@ -101,9 +92,13 @@ workflow_parameters:
       - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38']
     required: true
     description: |
-      Reference genome for alignment
-
+      Reference genome for annotation
 
+  - id: toppeak
+    type: integer
+    required: true
+    description: |
+      The number of top peaks to use for motif discovery.
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------